| Competition: | Russian Second Division |
| Season: | 1999 |
| Prevseason: | 1998 |
| Nextseason: | 2000 |
The 1999 Russian Second Division was the eighth edition of the Russian Second Division. There were 6 zones with 108 teams starting the competition (1 was excluded before the end of the season).
| Team | Head coach |
|---|---|
| FC Avtomobilist Noginsk | Igor Volchok |
| FC Spartak Shchyolkovo | Vladimir Yulygin |
| FC Saturn-d Ramenskoye | Viktor Nozdrin |
| FC Sportakademklub Moscow | Sergei Abramov |
| FC Zenit-2 St. Petersburg | Lev Burchalkin |
| FC Mosenergo Moscow | Valentin Sysoyev |
| FC Volochanin Vyshny Volochyok | Viktor Demidov |
| FC Dynamo-2 Moscow | Viktor Zernov/Leonid Ablizin |
| FC Spartak-2 Moscow | Nikolay Kiselyov |
| FC Dynamo Vologda | Leon Yagubyants |
| FC Neftyanik Yaroslavl | Valentin Volkov |
| FC Oazis Yartsevo | Vladimir Grigoryev (until July) Leonid Arkhipov (from July) |
| FC Dynamo-SPb St. Petersburg | Boris Rappoport |
| FC Lokomotiv-2 Moscow | Andrei Syomin |
| PFC CSKA-2 Moscow | |
| FC Energiya Velikiye Luki | Vladimir Kosogov |
| FC Torpedo-2 Moscow | Sergei Petrenko |
| FC Spartak Kostroma | Aleksandr Bogdanov (until June) Aleksei Yarovoy (June to August) Yu. Mukhortov (from September) |
| FC Volga Tver | Vladimir Seleznyov |
| FC Spartak-Peresvet Bryansk | Vyacheslav Perfilyev |
Andrey Movsisyan (FC Sportakademklub Moscow)| Team | Head coach |
|---|---|
| FC Spartak-Chukotka Moscow | Anatoli Shelest |
| FC Kolomna | Vadim Yastrebkov (until June), Fyodor Novikov (from June) |
| FC Kosmos Elektrostal | Aleksandr Logunov |
| FC Oryol | Vitali Koberskiy |
| FC Dynamo Bryansk | Igor Belonovich |
| FC Khimki | Ravil Sabitov (until August), Vadim Kots (caretaker, August), Ravil Sabitov (from September) |
| FC Spartak Tambov | Vladimir Kovylin |
| FC Lokomotiv Liski | Vladimir Ponomaryov (until August), Anatoli Vlasov (from August) |
| FC Fabus Bronnitsy | Aleksandr Antonov |
| FC Spartak Ryazan | Sergey Mushtruyev |
| FC Spartak-Telekom Shuya | Aleksandr Saitov |
| FC Lokomotiv Kaluga | Aleksandr Sakharov |
| FC Don Novomoskovsk | Igor Solovyov |
| FC Spartak Lukhovitsy | Sergei Malygin |
| FC Avangard Kursk | Aleksandr Galkin |
| FC Arsenal-2 Tula | Vyacheslav Ledovskikh |
| FC Titan Zheleznodorozhny | Dmitri Khazin (until July), Nikolai Pushkaryov (from July) |
| FC Torpedo Vladimir | Yuri Pyanov |
| FC Salyut-YuKOS Belgorod | Konstantin Afanasyev (until May), Vladimir Bulgakov (May to July), Vasili Golikov (from July) |
| Team | Head coach |
|---|---|
| FC Kuban Krasnodar | Soferbi Yeshugov |
| FC SKA Rostov-on-Don | Aleksandr Tumasyan |
| FC Kavkazkabel Prokhladny | Sergei Razaryonov |
| FC Avtodor Vladikavkaz | Yuri Gazzaev |
| FC Druzhba Maykop | Adam Natkho |
| FC Angusht Nazran | Timur Kuriyev (until July) Umar Markhiyev (from August) |
| FC Vityaz Krymsk | Kalin Stepanyan |
| FC Lokomotiv-Taym Mineralnye Vody | Aleksandr Ikayev (until April) Yuri Dukhovnov (April to August) Aleksandr Babayan (from August) |
| FC Rostselmash-2 Rostov-on-Don | |
| FC Dynamo Makhachkala | Magomed Isayev |
| FC Mozdok | Vladimir Arkalov |
| FC Slavyansk Slavyansk-na-Kubani | Vladimir Sinyagovsky |
| FC Shakhtyor Shakhty | Valeri Dzolov |
| FC Zhemchuzhina-2 Sochi | Anatoli Lyz |
| FC Venets Gulkevichi | Vasili Sidorenko |
| FC Nart Nartkala | Vladimir Kurashinov |
| FC Iriston Vladikavkaz | Ruslan Merdenov |
| FC Torpedo Taganrog | Anatoli Shabanov |
| FC Beshtau Lermontov | Sergei Shestakov, Viktor Vashchenko |
| FC Torpedo Georgiyevsk | Aleksandr Ivanchenko |
Iuri Gabiskiria (FC Kuban Krasnodar)| Team | Head coach |
|---|---|
| FC Lada Togliatti | Aleksandr Garmashov |
| FC Torpedo Pavlovo | Aleksandr Sarafannikov |
| FC Volga Ulyanovsk | Sergei Sedyshev |
| FC Energetik Uren | Viktor Pavlyukov |
| FC Iskra Engels | Dmitri Lobov |
| FC Diana Volzhsk | Valeri Bogdanov |
| FC Metallurg Vyksa | Yevgeni Popov |
| FC Biokhimik-Mordovia Saransk | Igor Shinkarenko |
| FC Khimik Dzerzhinsk | Valeri Volodin |
| FC Energiya Ulyanovsk | Yevgeni Yepifanov, Andrei Flaat |
| FC Balakovo | Gennadi Drozdov, Aleksandr Koreshkov, Vladimir Bibikov |
| FC Svetotekhnika Saransk | Aleksei Bessonov (until July) Valeri Guba (from July) |
| FC Torpedo Volzhsky | Aleksandr Khomutetskiy, Oleg Dudarin, Anatoli Kurbatov |
| FC Salyut Saratov | Vladimir Khoroltsev |
| FC Rotor-2 Volgograd | Yuri Marushkin |
| FC Dynamo-Mashinostroitel Kirov | Vasili Esaulov |
| FC Zenit Penza | |
| FC Torpedo Arzamas | Aleksandr Platonychev, Yuri Kamardin |
| FC Spartak-Telekom Shuya | Aleksandr Saitov |
| FC Druzhba Yoshkar-Ola | Radik Gadeyev |
| FC Progress Zelenodolsk | Aleksandr Klobukov |
| FC Rotor Kamyshin | Vladimir Bubnov |
| Team | Head coach |
|---|---|
| FC Nosta Novotroitsk | Leonid Shevchenko (until July) Boris Lavrov (from July) |
| FC Neftekhimik Nizhnekamsk | Ivan Butaliy |
| FC Zenit Chelyabinsk | Oleg Kudelin |
| FC Sodovik Sterlitamak | Sergei Maksimov |
| FC UralAZ Miass | Pyotr Nagayev |
| FC Metallurg-Metiznik Magnitogorsk | Aleksandr Kukushkin |
| FC Uralmash Yekaterinburg | Nikolai Agafonov |
| FC Uralets Nizhny Tagil | Lev Kutashov |
| FC Dynamo Perm | Andrei Boglayevskiy |
| FC KAMAZ-Chally Naberezhnye Chelny | Valeri Chetverik |
| FC Gazovik Orenburg | Aleksandr Korolyov |
| FC Dynamo Izhevsk | Stanislav Korotayev, Nikolai Vyutnov |
| FC Energiya Chaikovsky | Sergei Kleymyonov |
| FC Irtysh Tobolsk | Vitali Alkhazov, Vladimir Sizontov |
| FC Kurgan | |
| FC Neftyanik Pokhvistnevo | Georgi Verbovskiy |
Ruslan Uzakov (FC Nosta Novotroitsk)| Team | Head coach |
|---|---|
| FC Metallurg Novokuznetsk | Vladislav Sosnov |
| FC SKA-Energiya Khabarovsk |  Oleh Smolyaninov |
| FC Amur-Energiya Blagoveshchensk | Vyacheslav Kurtsayev |
| FC Sibiryak Bratsk | Valeri Tolchev |
| FC Chkalovets Novosibirsk | Sergei Iromashvili |
| FC Kuzbass Kemerovo | Sergei Vasyutin |
| FC Luch Vladivostok | Andrei Fedyakin |
| FC Zvezda Irkutsk | Sergei Muratov, Anatoly Bulgakov, Gennadi Vyazovtsev |
| FC Dynamo Barnaul | Viktor Volynkin, Vladimir Vorzhev |
| FC Irtysh Omsk | Artyom Amirdzhanov |
| FC Reformatsiya Abakan | Aleksandr Kishinevsky |
| FC Okean Nakhodka | Pavel Palatin (until July) Vladimir Susin (from July) |
| FC Zarya Leninsk-Kuznetsky | |
| FC Dynamo Omsk | Vyacheslav Martynov |
| FC Selenga Ulan-Ude | Valeri Mikhnov |
| FC Samotlor-XXI Nizhnevartovsk | Vladimir Kovbiy, Vyacheslav Mogilny, Aleksandr Kucherenko, Sergei Goncharov |
Ihor Yefremov (FC Amur-Energiya Blagoveshchensk)Nosta won 4–3 on aggregate and was promoted to the 2000 Russian First Division.----
Spartak-Chukotka won 5–2 on aggregate and was promoted to the 2000 Russian First Division.----
Lada Togliatti won 3–2 on aggregate and was promoted to the 2000 Russian First Division.----